SMTL ID : 3j2t.1

An improved model of the human apoptosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-7-mer

Ligands

7 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 19 residues within 4Å: Chain A: V.131, F.132, V.133, R.135, M.161, A.162, G.163, C.164, G.165, K.166, S.167, V.168, L.292, I.300, P.327, L.328, S.331, Y.365, D.366 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.133, A:R.135, A:R.135, A:G.163, A:C.164, A:G.165, A:K.166, A:S.167, A:S.167, A:S.167, A:V.168, A:S.331 ATP.2: 19 residues within 4Å: Chain B: V.131, F.132, V.133, R.135, M.161, A.162, G.163, C.164, G.165, K.166, S.167, V.168, L.292, I.300, P.327, L.328, S.331, Y.365, D.366 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:V.133, B:R.135, B:R.135, B:G.163, B:C.164, B:G.165, B:K.166, B:S.167, B:S.167, B:S.167, B:V.168, B:S.331 ATP.3: 19 residues within 4Å: Chain C: V.131, F.132, V.133, R.135, M.161, A.162, G.163, C.164, G.165, K.166, S.167, V.168, L.292, I.300, P.327, L.328, S.331, Y.365, D.366 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:V.133, C:R.135, C:R.135, C:G.163, C:C.164, C:G.165, C:K.166, C:S.167, C:S.167, C:S.167, C:V.168, C:S.331 ATP.4: 19 residues within 4Å: Chain D: V.131, F.132, V.133, R.135, M.161, A.162, G.163, C.164, G.165, K.166, S.167, V.168, L.292, I.300, P.327, L.328, S.331, Y.365, D.366 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:V.133, D:R.135, D:R.135, D:G.163, D:C.164, D:G.165, D:K.166, D:S.167, D:S.167, D:S.167, D:V.168, D:S.331 ATP.5: 19 residues within 4Å: Chain E: V.131, F.132, V.133, R.135, M.161, A.162, G.163, C.164, G.165, K.166, S.167, V.168, L.292, I.300, P.327, L.328, S.331, Y.365, D.366 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:V.133, E:R.135, E:R.135, E:G.163, E:C.164, E:G.165, E:K.166, E:S.167, E:S.167, E:S.167, E:V.168, E:S.331 ATP.6: 19 residues within 4Å: Chain F: V.131, F.132, V.133, R.135, M.161, A.162, G.163, C.164, G.165, K.166, S.167, V.168, L.292, I.300, P.327, L.328, S.331, Y.365, D.366 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:V.133, F:R.135, F:R.135, F:G.163, F:C.164, F:G.165, F:K.166, F:S.167, F:S.167, F:S.167, F:V.168, F:S.331 ATP.7: 19 residues within 4Å: Chain G: V.131, F.132, V.133, R.135, M.161, A.162, G.163, C.164, G.165, K.166, S.167, V.168, L.292, I.300, P.327, L.328, S.331, Y.365, D.366 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:V.133, G:R.135, G:R.135, G:G.163, G:C.164, G:G.165, G:K.166, G:S.167, G:S.167, G:S.167, G:V.168, G:S.331

7 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.8: 24 residues within 4Å: Chain H: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80, I.81, F.82, L.94 18 PLIP interactions: 18 interactions with chain H, Hydrophobic interactions: H:P.30, H:F.46, H:W.59, H:L.64, H:Y.67, H:L.68, H:M.80, H:F.82, H:L.94 Hydrogen bonds: H:G.41, H:Y.48, H:T.49, H:N.52, H:K.79 pi-Stacking: H:H.18, H:H.18, H:Y.67 Metal complexes: H:H.18 HEM.9: 24 residues within 4Å: Chain I: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80, I.81, F.82, L.94 18 PLIP interactions: 18 interactions with chain I, Hydrophobic interactions: I:P.30, I:F.46, I:W.59, I:L.64, I:Y.67, I:L.68, I:M.80, I:F.82, I:L.94 Hydrogen bonds: I:G.41, I:Y.48, I:T.49, I:N.52, I:K.79 pi-Stacking: I:H.18, I:H.18, I:Y.67 Metal complexes: I:H.18 HEM.10: 24 residues within 4Å: Chain J: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80, I.81, F.82, L.94 18 PLIP interactions: 18 interactions with chain J, Hydrophobic interactions: J:P.30, J:F.46, J:W.59, J:L.64, J:Y.67, J:L.68, J:M.80, J:F.82, J:L.94 Hydrogen bonds: J:G.41, J:Y.48, J:T.49, J:N.52, J:K.79 pi-Stacking: J:H.18, J:H.18, J:Y.67 Metal complexes: J:H.18 HEM.11: 24 residues within 4Å: Chain K: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80, I.81, F.82, L.94 18 PLIP interactions: 18 interactions with chain K, Hydrophobic interactions: K:P.30, K:F.46, K:W.59, K:L.64, K:Y.67, K:L.68, K:M.80, K:F.82, K:L.94 Hydrogen bonds: K:G.41, K:Y.48, K:T.49, K:N.52, K:K.79 pi-Stacking: K:H.18, K:H.18, K:Y.67 Metal complexes: K:H.18 HEM.12: 24 residues within 4Å: Chain L: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80, I.81, F.82, L.94 18 PLIP interactions: 18 interactions with chain L, Hydrophobic interactions: L:P.30, L:F.46, L:W.59, L:L.64, L:Y.67, L:L.68, L:M.80, L:F.82, L:L.94 Hydrogen bonds: L:G.41, L:Y.48, L:T.49, L:N.52, L:K.79 pi-Stacking: L:H.18, L:H.18, L:Y.67 Metal complexes: L:H.18 HEM.13: 24 residues within 4Å: Chain M: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80, I.81, F.82, L.94 18 PLIP interactions: 18 interactions with chain M, Hydrophobic interactions: M:P.30, M:F.46, M:W.59, M:L.64, M:Y.67, M:L.68, M:M.80, M:F.82, M:L.94 Hydrogen bonds: M:G.41, M:Y.48, M:T.49, M:N.52, M:K.79 pi-Stacking: M:H.18, M:H.18, M:Y.67 Metal complexes: M:H.18 HEM.14: 24 residues within 4Å: Chain N: K.13, C.14, Q.16, C.17, H.18, T.28, G.29, P.30, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.64, Y.67, L.68, T.78, K.79, M.80, I.81, F.82, L.94 18 PLIP interactions: 18 interactions with chain N, Hydrophobic interactions: N:P.30, N:F.46, N:W.59, N:L.64, N:Y.67, N:L.68, N:M.80, N:F.82, N:L.94 Hydrogen bonds: N:G.41, N:Y.48, N:T.49, N:N.52, N:K.79 pi-Stacking: N:H.18, N:H.18, N:Y.67 Metal complexes: N:H.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, S. et al., Changes in apaf-1 conformation that drive apoptosome assembly. Biochemistry (2013)

Release Date

2013-04-10

Peptides

Apoptotic protease-activating factor 1: ABCDEFG
Cytochrome c: HIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

Apoptotic protease-activating factor 1

Cytochrome c

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